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370 results • Page
3 of 8
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0
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0
replies
123
views
News:
Deadline Approaching: PETs for Public Health Challenge
privacy
public-health-challenge
updated 3 days ago by
Ram
43k • written 3 days ago by
polarise
▴ 380
0
votes
0
replies
130
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bioinfo
▴ 150
1
vote
2
replies
180
views
Problem with Sniffles pipeline and SV calling help
SV
sniffles
StructuralVariant
updated 3 days ago by
GenoMax
141k • written 3 days ago by
njornet
▴ 20
4
votes
0
replies
159
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
3 days ago by
Biostar
2.6k
2
votes
1
reply
212
views
Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
GSEA
pathways
GO-terms
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Manko47
• 0
4
votes
6
replies
382
views
Odd results with BLAST remote
blast
remote
NCBI
updated 2 days ago by
b.contreras.moreira
▴ 150 • written 3 days ago by
Begonia_pavonina
▴ 150
6
votes
8
replies
459
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 1 day ago by
dariober
14k • written 3 days ago by
manaswiniparija3
▴ 40
2
votes
0
replies
184
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
3 days ago by
Alexander
▴ 220
1
vote
1
reply
154
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 3 days ago by
GenoMax
141k • written 3 days ago by
eesiribloom
▴ 80
0
votes
0
replies
119
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
3 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
121
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
3 days ago by
adarsh_pp
▴ 40
2
votes
4
replies
324
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 3 days ago by
GenoMax
141k • written 4 days ago by
Sony
▴ 10
0
votes
0
replies
130
views
FreeBayes detection capacity
reads
freebayes
long
3 days ago by
quentinperriere
• 0
0
votes
2
replies
206
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
1 day ago by
DKA
▴ 40
0
votes
2
replies
229
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
3 days ago by
rj.rezwan
• 0
7
votes
7
replies
815
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 3 days ago by
Dunois
★ 2.5k • written 4 days ago by
AdviceSeeker
• 0
0
votes
0
replies
148
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
4 days ago by
Hien
• 0
0
votes
2
replies
257
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
2 days ago by
Koketso
• 0
1
vote
3
replies
390
views
Extracting data from a local NCBI taxonomy database
R
NCBI
xml
E-utilities
Blast
updated 4 days ago by
josev.die
▴ 60 • written 17 days ago by
Begonia_pavonina
▴ 150
0
votes
0
replies
174
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 4 days ago by
Ram
43k • written 4 days ago by
menyawino
• 0
0
votes
0
replies
150
views
News:
Online course: Network Analysis in R
NetworkAnalyis
R
4 days ago by
carlopecoraro2
★ 2.5k
1
vote
3
replies
305
views
Ensembl gene id conversion
biomart
ensembl
updated 2 days ago by
ATpoint
81k • written 4 days ago by
naveedhasan2000
• 0
1
vote
2
replies
287
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 3 days ago by
Istvan Albert
100k • written 4 days ago by
Jiang
• 0
85
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 21 hours ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
2
votes
3
replies
341
views
Deseq2 : Paired analysis or otherwise
linear-regression
paired-analysis
DESeq2
longitudinal-analysis
updated 3 days ago by
ATpoint
81k • written 5 days ago by
IM
• 0
2
votes
1
reply
275
views
How to highlight genes on genome visual reprezentation/what tool to use?
gene
genome
updated 5 days ago by
Alex Reynolds
35k • written 5 days ago by
natami
▴ 10
1
vote
1
reply
475
views
adding gene and CDS feature types in ensemble gtf annotation with transcript and exon features
GTF
GFF
transcript
CDS
exon
updated 5 days ago by
Pratik
★ 1.0k • written 5 days ago by
memy
▴ 20
0
votes
0
replies
193
views
Different flagstat number after using MergeBamAlignment
MergeBamAlignment
samtools
flagstat
5 days ago by
ThomasLam
• 0
3
votes
4
replies
349
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
Sony
▴ 10
0
votes
0
replies
172
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
5 days ago by
YiweiZhu
▴ 30
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 5 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
0
votes
0
replies
176
views
Somatic and Germline variant calling for tumor, normal and blood sample
germline
variants
somatic
updated 5 days ago by
Ram
43k • written 5 days ago by
anitharavichandran2211
• 0
0
votes
1
reply
218
views
Ciriquant not configuring hisat2 indexed files
ciriquant
updated 5 days ago by
Carlo Yague
8.6k • written 5 days ago by
Atul K.
• 0
1
vote
1
reply
244
views
How to handle more than 1 SRA Run per Experiment?
SRA
Preprocessing
updated 5 days ago by
ATpoint
81k • written 5 days ago by
Janmajay
• 0
0
votes
2
replies
297
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
5 days ago by
O.rka
▴ 710
0
votes
6
replies
510
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
3 days ago by
Dunois
★ 2.5k
1
vote
1
reply
257
views
How do I identify gene duplication or paralogs in an annotated reference genome assembly
blast
duplication
paralog
genome
updated 5 days ago by
sansan_96
▴ 80 • written 6 days ago by
brimaloney24
• 0
4
votes
7
replies
524
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 5 days ago by
Ram
43k • written 6 days ago by
AHerik
▴ 20
0
votes
0
replies
170
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 6 days ago by
GenoMax
141k • written 6 days ago by
zec018
• 0
5
votes
5
replies
833
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 6 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
0
votes
0
replies
186
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 6 days ago by
Ram
43k • written 6 days ago by
roussine
▴ 10
0
votes
0
replies
168
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
6 days ago by
Ronin
• 0
4
votes
4
replies
365
views
How do I install plink2 on a mac?
plink2
plink
updated 3 days ago by
zx8754
11k • written 6 days ago by
emilija.romic
▴ 10
0
votes
5
replies
454
views
Is it possible to set different tracks to the same scale in JBrowse
track
jbrowse
updated 6 days ago by
Ram
43k • written 8 days ago by
Jose
• 0
7
votes
7
replies
517
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 6 days ago by
Matthias Zepper
4.5k • written 6 days ago by
4fzcgueyp5
• 0
1
vote
2
replies
320
views
Forum:
VCF bulk handling
bcftools
SnpEff
WGS
VEP
VCF
1 day ago by
Javier
• 0
4
votes
13
replies
757
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 1 day ago by
BioinfGuru
★ 1.7k • written 7 days ago by
matteo.levorato
• 0
2
votes
1
reply
235
views
VEP annotation --per_gene allele choice
VEP
updated 6 days ago by
Ram
43k • written 6 days ago by
atariw
▴ 10
4
votes
4
replies
443
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 6 days ago by
damian.szk
▴ 50 • written 7 days ago by
rohitsatyam102
▴ 840
0
votes
2
replies
268
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 6 days ago by
Apollonia
• 0
370 results • Page
3 of 8
Recent Votes
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
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Recent Replies
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
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